Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains

Substantial progress has been made in the synthesis and characterization of various oligomeric molecules capable of autonomous folding to well-defined, repetitive secondary structures. It is now possible to investigate sequence-structure relationships and the driving forces for folding in these systems. Here, we present detailed analysis by X-ray crystallography, NMR, and circular dichroism (CD) of the helical structures formed by N-substituted glycine (or "peptoid") oligomers with alpha-chiral, aliphatic side chains. The X-ray crystal structure of a N-(1-cyclohexylethyl)glycine pentamer, the first reported for any peptoid, shows a helix with cis-amide bonds, approximately 3 residues per turn, and a pitch of approximately 6.7 A. The backbone dihedral angles of this pentamer are similar to those of a polyproline type I peptide helix, in agreement with prior modeling predictions. This crystal structure likely represents the major solution conformers, since the CD spectra of analogous peptoid hexamers, dodecamers, and pentadecamers, composed entirely of either (S)-N-(1-cyclohexylethyl)glycine or (S)-N-(sec-butyl)glycine monomers, also have features similar to those of the polyproline type I helix. Furthermore, this crystal structure is similar to a solution NMR structure previously described for a peptoid pentamer comprised of chiral, aromatic side chains, which suggests that peptoids containing either aromatic or aliphatic alpha-chiral side chains adopt fundamentally similar helical structures in solution, despite distinct CD spectra. The elucidation of detailed structural information for peptoid helices with alpha-chiral aliphatic side chains will facilitate the mimicry of biomolecules, such as transmembrane protein domains, in a distinctly stable form.     

Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis

Peptoids (N-substituted glycines) are an important class of biomimetic oligomers that have made a significant impact in the areas of combinatorial drug discovery, gene therapy, drug delivery, and biopolymer folding in recent years. Sequence-specific peptoid oligomers are easily assembled from primary amines by the solid-phase submonomer method. However, most amines that contain heterocyclic nitrogens in the side chain do not incorporate efficiently. We present here a straightforward revision of the submonomer method that allows efficient incorporation of unprotected imidazoles, pyridines, pyrazines, indoles, and quinolines into oligomers as long as 15 monomers in length. This improved method uses chloroacetic acid instead of bromoacetic acid in the acylation step of the monomer addition cycle, and allows for the incorporation of new side chains that should enable the synthesis of peptoids with entirely new properties.     

Heterocyclic amines for the construction of peptoid oligomers bearing multi-dentate ligands

Peptoids are oligomers of N-substituted glycine that can be readily assembled using haloacetic acids and primary amines as synthons. Here, we report the synthesis and characterization of three new heterocyclic amines, 2-(2,2′:6′,2″-terpyridine-4′-yloxy)ethylamine, 2-(1,10-phenanthroline-5-yloxy)ethylamine and 8-hydroxy-2-quinolinemethylamine, and their incorporation into a series of different peptoid oligomer sequences. Since the heterocycles are all known to coordinate metal ions, the peptidomimetic products are designed to bind metal species with the potential for applications in catalysis and materials science.     

Peptoid oligomers with alpha-chiral, aromatic side chains: sequence requirements for the formation of stable peptoid helices.

The achiral backbone of oligo-N-substituted glycines or "peptoids" lacks hydrogen-bond donors, effectively preventing formation of the regular, intrachain hydrogen bonds that stabilize peptide alpha-helical structures. Yet, when peptoids are N-substituted with alpha-chiral, aromatic side chains, oligomers with as few as five residues form stable, chiral, polyproline-like helices in either organic or aqueous solution. The adoption of chiral secondary structure in peptoid oligomers is primarily driven by the steric influence of these bulky, chiral side chains. Interestingly, peptoid helices of this class exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have taken advantage of this distinctive spectroscopic signature to investigate sequence-related factors that favor and disfavor stable formation of peptoid helices of this class, through a comparison of more than 30 different heterooligomers with mixed chiral and achiral side chains. For this family of peptoids, we observe that a composition of at least 50% alpha-chiral, aromatic residues is necessary for the formation of stable helical structure in hexameric sequences. Moreover, both CD and 1H-13C HSQC NMR studies reveal that these short peptoid helices are stabilized by the placement of an alpha-chiral, aromatic residue on the carboxy terminus. Additional stabilization can be provided by the presence of an "aromatic face" on the helix, which can be patterned by positioning aromatic residues with three-fold periodicity in the sequence. Extending heterooligomer chain length beyond 12-15 residues minimizes the impact of the placement, but not the percentage, of alpha-chiral aromatic side chains on overall helical stability. In light of these new data, we discuss implications for the design of helical, biomimetic peptoids based on this structural motif.     

Methylacrylate polymers with photochromic side chains containing heterocyclic sulfonamide substituted azobenzene

Methylacrylate monomers containing azobenzene groups with heterocyclic sulfonamide: sulfisomidyne (4-amino-N-[2,6-dimethylpyrimidyn-4-yl]benzenesulfonamide) and sulfamethoxazole (4-amino-N-[5-methylisoxazol-3-yl]benzenesulfonamide) substituents were synthesized. The monomers were used for preparation of homopolymers and copolymers with butyl 2-methylacrylate and 2-ethylhexyl acrylate. The materials obtained showed photochromic properties manifested by trans-cis isomerization of the side chain azobenzene fragments induced by illumination with unpolarized and polarized light. The decrease of the absorbance of the E(trans) form at ≈450 nm was observed and the materials tested were in form of thin films deposited onto glass.The isomerization of the polymers carried out during ellipsometric measurements showed the reversibility of the process in repeated illumination cycles with green laser light. The change of refractive index caused by illumination was in the range ≈0.005-0.008 as determined by ellipsometry.     

Photoinduced alignment of azobenzene moieties in the side chains of polyglutamate films

The ‘trans↔cis’ reversible photoisomerization process tends to align azobenzene derivatives perpendicular to the polarization direction of the pumping beam. It is shown that in the trans→cis optical transition the cis state is aligned perpendicular to the pumping light polarization. This is shown for spin-coated films of ‘hairy-rod’ polyglutamate with azobenzene moieties in the side chains. Photoselection in both trans and cis states is demonstrated using the attenuated total reflection method.     

Compatibility of coils and rods bearing flexible side chains

We present a theoretical treatment of nematic-isotropic phase equilibria in mixtures which consist of random coils and comblike polymers, the latter components being composed of a rigid backbone and flexible side chains. The mixing partition function is evaluated by using the Flory lattice model. The comblike component is characterized by the axial ratio x_r of its rigid main chain and the number of flexible side chains z, each containing m segments. The coiled component is described by its number of segments x_c. The net exchange energy of mixing is assumed to be zero; i.e., we consider athermal solutions. It is shown that the flexible side chains attached to the rigid main chains markedly enhance the compatibility in the isotropic phase. If the ratio of the volume fraction of the side chains to the volume fraction of the main chains is high enough, there is even a finite range of concentration where the random coils mix homogeneously with the comblike component. This is in contrast to mixtures of rods and coils, which have been shown by Flory to be incompatible over nearly the full range of composition. These conclusions hold true only when ordered states are involved. For comblike polymers with flexible backbones mixed with random coils in isotropic melts, the resulting free energy of mixing is given by the familiar Flory-Huggins expression.     

Photoresponsive upper-rim azobenzene substituted calix[4]resorcinarenes

Photoswitchable calix[4]resorcinarenes with different numbers of azo groups in the upper rim were synthesised by the reaction of bromomethylcavitand with 4-aminoazobenzene. UV-vis, ¹H and ¹³C NMR, MALDI TOF-MS spectral data have been used to elucidate the structures of compounds.     

Rigid rod polymers with flexible side chains. X. Thermotropic mesophases from aromatic stiff-chain polyamides bearing n-alkoxy side chains

The synthesis of stiff-chain poly(1,4-phenylene terephthalamide)s substituted by two as well as by four flexible side chains per repeating unit is described. The solubility of the materials bearing only two side chains is still very low. Appending of four side chains leads to polyamides which dissolve in common organic solvents. All polyamides reported herein form layered structures in the solid state as well as in the mesophase. Polyamides with two side chains have a very weak tendency for crystallization and do not exhibit a transition to the isotropic state even for the longest side chains. Polyamides with four side chains show three reversible thermal transitions: a disordering transition of the side chains, a transition to a layered, smectic-like mesophase, and finally the transition to an isotropic melt. It is shown that the phase behavior of these materials is mainly governed by the strong segregation of main- and side-chains which can be compared best to the microphase separation in block copolymers. © 1993 John Wiley & Sons, Inc.     

Photomodulated chiral induction in helical azobenzene oligomers

Appending L-alanine to the terminal positions of a helical azobenzene oligomer produced a P helical bias, which increased with oligomer length. Irradiation gave rise to E-->Z isomerization of the terminal azo linkages, which displaced the stereogenic center of L-Ala from the helix backbone and suppressed chiral induction. Theoretical simulations of the CD spectrum of the P helical conformation are in qualitative agreement with the experimental spectra.     

Solid-phase and solution-phase syntheses of oligomeric guanidines bearing peptide side chains

[reaction: see text] Synthetic strategies for preparing N,N'-bridged oligomeric guanidines bearing peptide side chains both on solid support and in solution are presented. Monomers are prepared from common alpha-amino acids and therefore contain conventionally protected peptide side chains. The side chains include alkyl, aromatic, hydroxyl, amino, carboxylic acid, and amide functional groups. Oligomer elongation utilizes acid-sensitive sulfonyl activated thiourea through the formation of carbodiimide intermediate. With proper preparation of monomers, synthesis of oligomer can be performed in two directions (equivalent to N to C terminal or C to N terminal in a peptide sequence) with excellent efficiency.     

Synthesis of beta-lactams bearing functionalized side chains from a readily available precursor

The reaction of chlorosulfonyl isocyanate (CSI) with alkenes provides beta-lactams in quantity, and the products have frequently been used for ring-opening polymerization to generate nylon-3 materials. Prior uses of this approach have focused almost entirely on beta-lactams with purely hydrocarbon substitutents. We show how a variety of beta-lactams bearing protected polar substituents can be generated from CSI-derived building blocks.     

Two-component fibers/gels and vesicles formed from hetero-double-helices of pseudoenantiomeric ethynylhelicene oligomers with branched side chains

A methodology for the formation of fibers/gels and vesicles by molecular assembly and for controlling their properties is presented. Two-component systems of pentamer (P)-5 and tetramer (M)-4 pseudoenantiomeric ethynylhelicenes with decyloxycarbonyl (D) and 4-methyl-2-(2-methylpropyl)-1-pentyloxycarbonyl (bD) side-chains have been examined. Distinct aggregates were formed by changing the solvent for the three combinations of (P)-bD-5/(M)-bD-4, (P)-D-5/(M)-bD-4, and (P)-D-5/(M)-D-4. In toluene, (P)-bD-5/(M)-bD-4, (P)-D-5/(M)-bD-4, and (P)-D-5/(M)-D-4 all formed gels and fibrous assemblies were observed by AFM. The minimum gel-forming concentration (MGC) decreased in the order (P)-bD-5/(M)-bD-4>(P)-D-5/(M)-bD-4>(P)-D-5/(M)-D-4. In diethyl ether, vesicular formation was observed by dynamic light scattering (DLS), AFM, and TEM, and the size of the vesicles decreased in the order (P)-bD-5/(M)-bD-4>(P)-D-5/(M)-bD-4>(P)-D-5/(M)-D-4. Both fiber/gel and vesicle formation were accompanied by enhanced CDs and redshifted UV/Vis absorption bands with a change in color to deep yellow. These are novel two-component oligomeric systems that form assemblies of fibers/gels or vesicles depending on the solvent, and the structures and properties of the assemblies can be fine-tuned by changing the combination of oligomers. In m-difluorobenzene, a homogeneous solution was obtained with (P)-D-5/(M)-bD-4, which again exhibits enhanced CDs and redshifted UV/Vis absorptions. Vapor pressure osmometry analysis showed the formation of a bimolecular heteroaggregate. The study has indicated that pseudoenantiomeric oligomers form hetero-double-helices that hierarchically assemble to form fibers/gels and vesicles.     

Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.     

Photoresponsive ion gating function of an azobenzene polyelectrolyte multilayer spin-self-assembled on a nanoporous support

The fabrication of a polyelectrolyte multilayer (PEM) on a porous membrane was successfully improved by using spin-coating electrostatic self-assembly. Surprisingly, the quality of the PEM film obtained on the nanoporous alumina substrate (i.e., its thickness and surface morphology) was comparable to that of a film deposited on silicon. An optical molecular switch that acts as an ion-gating channel was realized using a PEM membrane deposited layer-by-layer on an alumina support. One of the layer components of this device was a poly(acrylamide) copolymer containing an azobenzene chromophore, which is known to reveal strong voluminous expansion and contraction during light-induced reversible cis/trans isomerizations. The permeability of the bulk SO4(2-) ions was found to be sensitive to the changed channel sizes; for instance, the ion-permeation rate of SO4(2-) increased about 1.6 times after UV irradiation of the PEM, whereas that of the Cl- ion increased only 1.2 times. In the study, it was successfully demonstrated that the ion flow through the PEM membrane could be reversibly switched on and off over several azobenzene isomerization cycles.     

Photoresponsive porphyrin-imprinted polymers prepared using a novel functional monomer having diaminopyridine and azobenzene moieties

A novel photoresponsive functional monomer bearing diaminopyridine and azobenzene moieties was synthesized and applied to the preparation of photo-regulated molecularly imprinted polymers, which can recognize porphyrin derivatives through hydrogen bonding. The binding affinity of the imprinted cavities was regulated by UV irradiation, suggesting that azobenzene groups located inside the binding sites worked as photosensitizers and the trans-cis isomerization could regulate the affinity for the target compounds. Repetitive binding of the target compound to trans-IP and cis-IP was directly monitored by slab optical waveguide spectroscopy and the photo-mediated regulation of binding affinity was successfully confirmed.     

Clickity-click: highly functionalized peptoid oligomers generated by sequential conjugation reactions on solid-phase support

N-Substituted glycine peptoid oligomers were used as substrates for azide-alkyne [3 + 2] cycloaddition conjugation reactions and then elaborated through additional rounds of oligomerization and cycloaddition. This novel sequential conjugation technique allowed for the generation of complex peptidomimetic products in which multiple heterogeneous pendant groups were site-specifically positioned along the oligomer scaffold. Studies of a water-soluble estradiol-ferrocene peptoid conjugate demonstrated a potential application for the modular synthesis of biosensors.